Handle more warnings

Punt on the issue of warnings with the minimum build

Handle warnings in measure pkg

Fix the rank filter test by forcing a random seed in the function

Compare as boolean in imread test

Import loadmat in test_setup to avoid warning

Use a setup method for imread plugin test

Revoke unintended changes

Fix indentation to appease jni

More indentation fixes

Fix unintentional comment out

setup.py

@@ -149,7 +149,7 @@ if __name__ == "__main__":
 
         configuration=configuration,
         install_requires=[
-            "six>=%s" % '.'.join(str(d) for d in DEPENDENCIES['six'])
+            "six>=%s" % DEPENDENCIES['six']
         ],
         packages=setuptools.find_packages(exclude=['doc']),
         include_package_data=True,

skimage/_shared/testing.py

@@ -179,12 +179,14 @@ def mono_check(plugin, fmt='png'):
 
 
 def setup_test():
-   warnings.simplefilter('error')
-   with all_warnings():
+    warnings.simplefilter('error')
+    with all_warnings():
        from scipy import signal, ndimage, special, optimize, linalg
+       from scipy.io import loadmat
        from skimage import filter, viewer, data
        data.moon()
-
+    if os.environ.get('TRAVIS_PYTHON_VERSION', None) == '2.7':
+        warnings.simplefilter('default') 
 
 if __name__ == '__main__':
     color_check('pil')

skimage/filters/rank/tests/test_rank.py

@@ -13,12 +13,12 @@ np.random.seed(0)
 
 
 def test_all():
-
-  with all_warnings():  # precision loss
-    check_all()
+    with all_warnings():  # precision loss
+        check_all()
 
 
 def check_all():
+    np.random.seed(0)
     image = np.random.rand(25, 25)
     selem = morphology.disk(1)
     refs = np.load(os.path.join(skimage.data_dir, "rank_filter_tests.npz"))
@@ -159,7 +159,7 @@ def test_bitdepth():
     for i in range(5):
         image = np.ones((100, 100), dtype=np.uint16) * 255 * 2 ** i
         with all_warnings():  # bit depth
-          rank.mean_percentile(image=image, selem=elem, mask=mask,
+            rank.mean_percentile(image=image, selem=elem, mask=mask,
                                out=out, shift_x=0, shift_y=0, p0=.1, p1=.9)
 
 
@@ -270,7 +270,7 @@ def test_compare_ubyte_vs_float():
         func = getattr(rank, method)
         out_u = func(image_uint, disk(3))
         with all_warnings():  # precision loss
-          out_f = func(image_float, disk(3))
+            out_f = func(image_float, disk(3))
         assert_equal(out_u, out_f)
 
 
@@ -283,9 +283,9 @@ def test_compare_8bit_unsigned_vs_signed():
     image[image > 127] = 0
     image_s = image.astype(np.int8)
     with all_warnings():  # precision loss
-      image_u = img_as_ubyte(image_s)
+        image_u = img_as_ubyte(image_s)
 
-      assert_equal(image_u, img_as_ubyte(image_s))
+        assert_equal(image_u, img_as_ubyte(image_s))
 
     methods = ['autolevel', 'bottomhat', 'equalize', 'gradient', 'maximum',
                'mean', 'subtract_mean', 'median', 'minimum', 'modal',
@@ -295,8 +295,8 @@ def test_compare_8bit_unsigned_vs_signed():
         func = getattr(rank, method)
 
         with all_warnings():  # sign loss
-          out_u = func(image_u, disk(3))
-          out_s = func(image_s, disk(3))
+            out_u = func(image_u, disk(3))
+            out_s = func(image_s, disk(3))
         assert_equal(out_u, out_s)
 
 
@@ -487,11 +487,11 @@ def test_entropy():
     data = np.tile(
         np.reshape(np.arange(4096), (64, 64)), (2, 2)).astype(np.uint16)
     with all_warnings():  # bitdepth
-      assert(np.max(rank.entropy(data, selem)) == 12)
+        assert(np.max(rank.entropy(data, selem)) == 12)
 
     # make sure output is of dtype double
     with all_warnings():  # bitdepth
-      out = rank.entropy(data, np.ones((16, 16), dtype=np.uint8))
+        out = rank.entropy(data, np.ones((16, 16), dtype=np.uint8))
     assert out.dtype == np.double
 
 
@@ -523,9 +523,9 @@ def test_16bit():
         value = 2 ** bitdepth - 1
         image[10, 10] = value
         with all_warnings():  # bitdepth
-          assert rank.minimum(image, selem)[10, 10] == 0
-          assert rank.maximum(image, selem)[10, 10] == value
-          assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
+            assert rank.minimum(image, selem)[10, 10] == 0
+            assert rank.maximum(image, selem)[10, 10] == value
+            assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
 
 
 def test_bilateral():

skimage/io/_plugins/pil_plugin.py

@@ -48,8 +48,7 @@ def imread(fname, dtype=None, img_num=None, **kwargs):
     im = Image.open(fname)
     try:
         # this will raise an IOError if the file is not readable
-        #im.getdata()[0]
-        pass
+        im.getdata()[0]
     except IOError:
         site = "http://pillow.readthedocs.org/en/latest/installation.html#external-libraries"
         raise ValueError('Could not load "%s"\nPlease see documentation at: %s' % (fname, site))

skimage/io/tests/test_imread.py

@@ -11,13 +11,16 @@ import skimage.io as sio
 
 try:
     import imread as _imread
-    use_plugin('imread')
 except ImportError:
     imread_available = False
 else:
     imread_available = True
 
-np.random.seed(0)
+
+def setup():
+    if imread_available:
+        np.random.seed(0)
+        use_plugin('imread')
 
 
 def teardown():
@@ -54,7 +57,7 @@ def test_bilevel():
     expected[::2] = 1
 
     img = imread(os.path.join(data_dir, 'checker_bilevel.png'))
-    assert_array_equal(img, expected)
+    assert_array_equal(img.astype(bool), expected)
 
 
 class TestSave:

skimage/measure/tests/__init__.py

@@ -0,0 +1,2 @@
+from skimage._shared.testing import setup_test
+setup_test()